#' @title J48 Decision Tree

#' @description The decision tree analysis is implemented over a training

#'   dataset, which consisted of the DEGs obtained by either SAMseq or the

#'   binomial differential expression.

#' @export

#' @param data A data frame resulted from running the function ClassVectoringDT.

#' @param quiet If `TRUE`, suppresses intermediary output

#' @param plot If `FALSE`, suppresses plot output

#' @importFrom RWeka J48

#' @importFrom graphics plot

#' @return Information about the J48 model and, by default, a plot of the

#'   decision tree.

J48DT <- function(data, quiet = FALSE, plot = TRUE) {

  msg <- NULL

  if (!is.data.frame(data)) {

    msg <- c(msg, "input data must be data.frame")

  } else if (nrow(data) < 2) {

    msg <- c(msg, "input data must have more than one row")

  } else if (ncol(data) < 2) {

    msg <- c(msg, "input data must have more than one column")

  } else if (sum(apply(is.na(data), 1, sum)) > 0) {

    msg <- c(msg, "NAs are not allowed in input data")

  } else if (sum(apply(data, 1, min)) < 0) {

    msg <- c(msg, "negative values are not allowed in input data")

  }

  if (is.null(msg)) TRUE else msg

  exp.df <- as.data.frame(t(data))

  exp.df$classVector <- factor(colnames(data))

  j48.model <- J48(classVector ~ ., exp.df)

  if (!quiet) print(j48.model)

  if (plot) plot(j48.model)

  return(j48.model)

}